T-RFLP analysis of bacterial communities in cyclodextrin-amended bioreactors developed for biodegradation of polychlorinated biphenyls

Environmental, Microbiological, and Immunological Features of Bacterial Biofilms Associated with Implanted Medical Devices

The spread of biofilms on medical implants represents one of the principal triggers of persistent and chronic infections in clinical settings, and it has been the subject of many studies in the past few years, with most of them focused on prosthetic joint infections. We review here recent works on biofilm formation and microbial colonization on a large variety of indwelling devices, ranging from heart valves and pacemakers to urological and breast implants and from biliary stents and endoscopic tubes to contact lenses and neurosurgical implants. We focus on bacterial abundance and distribution across different devices and body sites and on the role of environmental features, such as the presence of fluid flow and properties of the implant surface, as well as on the interplay between bacterial colonization and the response of the human immune system.

Analysis of biofilm bacterial communities responsible for carbon removal through a reactor cascade treating wastewater

In this study molecular microbiological and multivariate statistical analyses were carried out to determine the structure and dynamics of bacterial communities through a biofilm based, pilot-scale wastewater treatment cascade system comprised of eight reactors. Results indicated a vertical as well as horizontal differentiation of biofilm bacterial communities within individual reactors and through the reactor series, respectively. The richness of biofilm samples taken from dissolved oxygen rich sections of reactors were relatively lower than of samples taken from less oxygenized sections (one-way ANOVA P = 0.07). The Euclidean distance based one-way ANOSIM pointed out that in bacteriological point of view: (1) no statistically significant difference could be observed among the first five reactors (P ≥ 0.1); (2) the first seven reactors differed significantly from the last reactor, (P ≤ 0.03); (3) reactors 1 and 2 differed significantly from reactors 6 and 7 (P ≈ 0.02) and (4) reactor 3 from reactor 7 (P ≈ 0.03). 16S rRNA gene cloning revealed that through the cascade system the initially dominant heterotrophic bacteria (Acinetobacter, Acidovorax, Parabacteroides, Thauera, Desulfobacterium and Desulfomicrobium) were gradually replaced or supplemented by autotrophic nitrifying bacteria (Nitrosomonas, 'Candidatus Nitrotoga' and Nitrospira). Our results indicate that the vertical alteration of bacterial community structure within a particular reactor was driven by the alteration of dissolved oxygen concentration, while the horizontal alteration of bacterial community structure through the cascade system was driven mainly by the gradually decreasing dissolved organic matter content and increasing dissolved oxygen concentration.

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the long-term impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the α-, β-, γ-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the β-, γ-Proteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.

Bioaugmentation for polyacrylamide degradation in a sequencing batch reactor and contact oxidation reactor

In the present study, one PAM degrading bacterial strain, originally named HWBI, was isolated from an activated sludge sample and used as an exogenous bacteria for bioaugmentation. The strain was primarily identified as Bacillus cereus. One contact oxidation reactor (COR) and one sequencing batch reactor (SBR) were bioaugmented with the HWBI, respectively, and the performance of the bioaugmented systems for PAM removal were investigated under long term operation. Results showed that for the COR augmented with HWBI, 70% of PAM was removed at the end of the 7th day after a single inoculation, and the removal efficiency remained at approximately 70% in the following 45 days after a single inoculation. For the SBR augmented with HWBI, 70% of PAM was removed at the end of the first operation cycle, and the removal remained at approximately 70% in the following eight cycles after a single inoculation. The results indicate that HWBI is an efficient exogenous bacteria for bioaugmentation for PAM removal. Although the COR and SBR were both appropriate reactors that may be used for treatment of PAM using bioaugmentation, the COR was found to be a more time-efficient method compared to the SBR. A molecular screening technique, terminal restriction fragment length polymorphism (T-RFLP), was applied to track the supplemented bacterial strain and to evaluate the effects of bioaugmentation on the microbial communities and to investigate the optimal bioaugmentation strategy.

Succession of bacterial community along with the removal of heavy crude oil pollutants by multiple biostimulation treatments in the Yellow River Delta, China

Multiple biostimulation treatments were applied to enhance the removal of heavy crude oil pollutants in the saline soil of Yellow River Delta. Changes of the soil bacterial community were monitored using the terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The 140-day microcosm experiments showed that low C:N:P ratio, high availability of surfactant and addition of bulking agent significantly enhanced the performance, leading to the highest total petroleum hydrocarbon removal. Meanwhile, the bacterial community was remarkably changed by the multiple biostimulation treatments, with the Deltaproteobacteria, Firmicutes, Actinobacteria, Acidobacteria and Planctomycetes being inhibited and the Alpha- and Beta-proteobacteria and some unknown Gammaproteobacteria bacteria being enriched. In addition, different hydrocarbon-degraders came to power in the following turn. At the first stage, the Alcanivorax-related Gammaproteobacteria bacteria dominated in the biostimulated soil and contributed mainly to the biodegradation of easily degradable portion of the heavy crude oil. Then the bacteria belonging to Alphaproteobacteria, followed by bacteria belonging to Candidate division OD1, became the dominant oil-degraders to degrade the remaining recalcitrant constituents of the heavy crude oil.

Changes of diversity pattern of proteolytic bacteria over time and space in an agricultural soil

The genetic heterogeneity of neutral metalloprotease (npr) gene fragments from soil proteolytic bacteria was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. Terminal restriction fragment length polymorphism (T-RFLP) analyses of polymerase chain reaction-amplified npr gene fragments were applied to study the dynamic of the npr gene pool with regard to environmental conditions. The aim of this study was to relate differences in npr community structure and richness to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. T-RFLP analysis revealed a noticeable seasonal variability in the community structure of npr-containing bacteria. The data suggest that the composition of the npr proteolytic bacterial population in July differed from those at the other dates. Additionally, the diversity of npr genes decreased with increasing soil depth revealing the highest values in upper layers. The reasons behind the observed patterns in the community structure might be mainly seasonal and vertical variation of the quantity and heterogeneity of available substrates as well as spatial isolation caused by a varying water amount and the connectivity of soil particles among the soil profile. Sequencing and phylogenetical analysis of 120 npr clones from the top soils collected in July revealed that most of the clones exhibit only poor homology to npr genes of isolates previously obtained from various environments, indicating the presence of until now uncharacterized npr coding proteolytic bacteria at the study site.

Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.

A review on slurry bioreactors for bioremediation of soils and sediments

The aim of this work is to present a critical review on slurry bioreactors (SB) and their application to bioremediation of soils and sediments polluted with recalcitrant and toxic compounds. The scope of the review encompasses the following subjects: (i) process fundamentals of SB and analysis of advantages and disadvantages; (ii) the most recent applications of SB to laboratory scale and commercial scale soil bioremediation, with a focus on pesticides, explosives, polynuclear aromatic hydrocarbons, and chlorinated organic pollutants; (iii) trends on the use of surfactants to improve availability of contaminants and supplementation with degradable carbon sources to enhance cometabolism of pollutants; (iv) recent findings on the utilization of electron acceptors other than oxygen; (v) bioaugmentation and advances made on characterization of microbial communities of SB; (vi) developments on ecotoxicity assays aimed at evaluating bioremediation efficiency of the process.From this review it can be concluded that SB is an effective ad situ and ex situ technology that can be used for bioremediation of problematic sites, such as those characterized by soils with high contents of clay and organic matter, by pollutants that are recalcitrant, toxic, and display hysteretic behavior, or when bioremediation should be accomplished in short times under the pressure and monitoring of environmental agencies and regulators. SB technology allows for the convenient manipulation and control of several environmental parameters that could lead to enhanced and faster treatment of polluted soils: nutrient N, P and organic carbon source (biostimulation), inocula (bioaugmentation), increased availability of pollutants by use of surfactants or inducing biosurfactant production inside the SB, etc. An interesting emerging area is the use of SB with simultaneous electron acceptors, which has demonstrated its usefulness for the bioremediation of soils polluted with hydrocarbons and some organochlorinated compounds. Characterization studies of microbial communities of SB are still in the early stages, in spite of their significance for improving reactor operation and design optimization.We have identified the following niches of research needs for SB in the near and mid term future, inter alia: (i) application of SB with sequential and simultaneous electron acceptors to soils polluted with contaminants other than hydrocarbons (i.e., pesticides, explosives, etc.), (ii) evaluation of the technical feasibility of triphasic SB that use innocuous solvents to help desorbing pollutants strongly attached to soils, and in turn, to enhance their biodegradation, (iii) gaining deeper insight of microbial communities present in SB with the intensified application of molecular biology tools such as PCR-DGGE, PCR-TGGE, ARDRA, etc., (iv) development of more representative ecotoxicological assays to better assess the effectiveness of a given bioremediation process.

The use of molecular techniques to characterize the microbial communities in contaminated soil and water

Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed.

Bacterial community structure in soils contaminated by polycyclic aromatic hydrocarbons

Bacterial community structure was examined in polycyclic aromatic hydrocarbon (PAH) contaminated soil taken from a timber treatment facility in southern Ireland. Profiles of soil bacterial communities were generated using a molecular fingerprinting technique, terminal restriction fragment length polymorphism (TRFLP), and results were interpreted using sophisticated multivariate statistical analysis. Findings suggested that there was a correlation between PAH structure and bacterial community composition. Initial characterisation of soil from the timber treatment facility indicated that PAH contamination was unevenly distributed across the site. Bacterial community composition was correlated with the type of PAH present, with microbial community structure associated with soil contaminated with two-ringed PAHs only being distinctly different to communities in soils contaminated with multi-component PAH mixtures. Typically the number of bacterial ribotypes detected in samples did not appear to be adversely affected by the level of contamination.

Development and assessment of an innovative soil-washing process based on the use of cholic acid-derivatives as pollutant-mobilizing agents

Surfactant-aided soil washing is often proposed for the restoration of aged organic pollutant-contaminated soils. As many of commercial surfactants have been found to be toxic and recalcitrant, the opportunity to use in this process cheap, non-toxic, and biodegradable pollutant-mobilizing agents, such as deoxycholic acid (DA), bovine bile (BB), and the residue resulting from DA extraction from BB (BBR), was studied in this work. A soil historically contaminated by chlorinated anilines and benzenes, thiophenes, and several polycyclic aromatic hydrocarbons was suspended at 15% w/v and washed in water or water amended at 1.0% (w/v) with DA, BB, BBR, or Triton X-100 (TX). The resulting effluents were supplemented with nutrients and subjected to aerobic bioremediation. The biogenic agents enhanced the water pollutant elution potential by 230/440%. TX enhanced the same parameter by about 540%; however, it mediated a lower depletion of the initial soil ecotoxicity and a more extensive mobilization of soil constituents with respect to the biogenic agents. Furthermore, TX adversely affected the biotreatability of resulting effluents, by adversely affecting the growth of cultivable bacterial biomass and the structure of eubacterial community of the effluent. On the contrary, the biogenic agents, and in particular DA and BB, enhanced the effluents bioremediation, by sustaining the growth and increasing the complexity of the effluent eubacterial communities. Thus, DA and BB are very promising additives for an effective and environmental friendly soil washing treatment of aged (chloro)organics contaminated soils.